Check engine light stays on and I have replaced the smog pump

Question edited for clarity.
Question moved to model category.

Did you clear the code with a Scan Tool after replacing the valves?

The 1998-2001 Chevrolet Tahoe has a known issue with the air pump check valve which causes illumination of the check engine light. There are no notable symptoms, but the vehicle will not pass state inspection or smog testing. When the valve fails, it sticks closed, and the computer sets the code P1416.Dec 10, 2016

Check Engine Light and Code P1416 on Chevrolet Tahoe

..

What ? the monitors aren't set ? Need to do drive cycle to get them to set . Do you have a check engine light lit ?

Ford Motor Company Driving Cycle

How do you know the pump is defective, what is the code?

The smog check requires a visual inspection of your check engine light. It has to come on for a bulb check at startup to make sure it's working. But, the light must go out after starting the engine(it cannot stay on after the engine starts during a smog check). If the check engine light fails either of these two tests, the vehicle will fail the smog check inspection.
You need to have the cause of your inoperative check engine light diagnosed and repaired.

Codes and the CEL can be erased with the same scanner used to retrieve the codes. It is a separate function of scanners.

I would think you can get it reflashed at the dealer.

http://wiki.answers.com/Q/Secondary_air_pump_dodge_stratus

code will keep returning until repair is correct or you have another problem

what you could start with is checking to see what trouble codes are being logged for this vehicle...if the engine light stays on, it means the ecu is registering a fault......by the means of a trouble code...now the trouble code doesnt tell you how to fix it, but it does give you the direction to go down...judst wondering if you have tried to obtain the trouble codes

No the water pump will not affect the smog test. You probably failed the idle?
Usually with this age of vehicle you can replace the o2 (oxygen) sensor and it will pass. Cleaning the MAF if it has one cant hurt either if you do it right.